Well, my /usr/share/unattended-upgrades script looks like this now:
...
    # run
    start_time = time.time()
    while True: 
        subprocess.call(["/bin/plymouth","message", "--text", 
"unattended-upgrades were here"])
...

I don't see the message every time I shut down the machine, but it's
likely because this line is executed before Plymouth is up. I'll use the
lock file test you provided and try again.

I started testing this because I saw similar problem on a machine
connected to the internet via proxy which silently refused most
connections, including Ubuntu repositories. The machine just kept
showing the splash and didn't shut down for a long time. But the lock
file should be present in this case, so I blamed Plymouth.

I wonder why non-SUID script didn't work for me in the beginning. I
tested in on this and on my plymouth-greeter script, both of them didn't
work without SUID.

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https://bugs.launchpad.net/bugs/677516

Title:
  No sign of updates still being installed when shutting down

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